OK, you may be right it's only cosmetic.
The warning message doesn't show up on x86_64 because the bigger value of 'max_join_size' is allowed there.
Looking at the defaults from both 5.0.45.i386 and 5.0.77.i386 show that the effective 'max_join_size' has not changed. So yes, it seems fine despite the warning message.

Thanks --- the upstream report seems rather confused about whether there's any real effect beyond the warning message, so I was wondering if you'd seen anything. As things stand, I doubt we'd bother to fix this short of a version update; but if you see any worse effects please note them here.

Our production box which is now running 5.0.77 on i386 seems to behave exactly the same way as it did with 5.0.45. The DB size is ~2G at an average rate of ~320 queries per second. I guess if some parameter was really wrong we should have seen it now somehow.

This request was evaluated by Red Hat Product Management for
inclusion in the current release of Red Hat Enterprise Linux.
Because the affected component is not scheduled to be updated in the
current release, Red Hat is unfortunately unable to address this
request at this time. Red Hat invites you to ask your support
representative to propose this request, if appropriate and relevant,
in the next release of Red Hat Enterprise Linux.

We are seeing the same issue, but it seems only to exist on 32 bit systems.
As this issue was introduced with a MySQL update of RHEL around or before
2009-09-20, I've now cross-filed this issue as Service Request 00474460.

This request was evaluated by Red Hat Product Management for
inclusion in the current release of Red Hat Enterprise Linux.
Because the affected component is not scheduled to be updated in the
current release, Red Hat is unfortunately unable to address this
request at this time. Red Hat invites you to ask your support
representative to propose this request, if appropriate and relevant,
in the next release of Red Hat Enterprise Linux.